Posted
by
timothy
on Sunday May 09, 2010 @02:32PM
from the can't-we-send-it-to-mars-and-settle-this? dept.

separsons writes "Researchers at the Lawrence Livermore National Laboratory recently unveiled a three-inch-long bio-detector than can scan for 3,000 different types of viruses and bacteria in just 24 hours. The device, dubbed the Lawrence Livermore Microbial Detection Array (LLMDA), boasts significant advantages over traditional bio-detectors, which can only identify a maximum of 50 pathogens. The three-inch-long glass slide is packed with 388,000 probes that can detect more than 2,000 viruses and 900 bacteria. The device may have huge implications in identifying agents released during biological and chemical attacks. Plus, in more everyday uses, LLMDA can ensure food, drug and vaccine safety and help diagnose medical problems. Scientists' next version of LLMDA is even more impressive: A new bio-detector will be lined with 2.1 million probes that can scan for 5,700 viruses and thousands of bacteria as well as fungi and protozoa."

The device may have huge implications in identifying agents released during biological and chemical attacks
Yes, don't we all just hate those attacks we're suffering all the time. Finally the LLNL is spending money where it's really needed.

Fixed that for them. AFAICT, the only biological attacks in the USA have been made by Federal employees.

Then what you know is wrong. Another who has worked in the same lab and is no longer restricted by his contract has come forward and stated is would be impossible for the Anthrax to have been made there. Furthermore, the DNA of the Anthrax was proved to not have come from that facility; though likely to be very closely related. According to the co-worker, it would have taken him years and the majority of the lab to have manufactured that much Anthrax in that tiny lab. As such, it is literally impossible for

AFAICT, the only biological attacks in the USA have been made by Federal employees.

Then what you know is wrong. Another who has worked in the same lab and is no longer restricted by his contract has come forward and stated is would be impossible for the Anthrax to have been made there. Furthermore, the DNA of the Anthrax was proved to not have come from that facility; though likely to be very closely related.

Fortunately anthrax is just one more disease that people have been getting for thousands of years. Livestock farmers in Iran and Iraq still get it. We've survived plagues before. We'll survive again (most of us). But if the U.S. government hadn't done the research, it wouldn't be a problem.

The USSR was also doing that research. And as you point out, anyone else can too.

Nobody knew for sure that it was possible to weaponize anthrax until we had done it. Now we've shown that it's possible, and we've shown how to do it.

Wrong. The USSR had weaponized Anthrax long before the US did. And to be absolutely clear, creating a quantity of anthrax does not mean its been weaponized. There is a HUGE difference. The mailing of anthrax absolutely is NOT weaponization.

You need to keep in mind, the bulk of our bio-research ("germ warfare") was as a directly response to the USSR's massive program (largest in the world). They invested heavily because they realized early on they could never keep nuclear pace. So in response to the USSR's b

Now, as a result of the USMRIID's biological warfare program, terrorists know that it's possible to convert anthrax into an easily-inhalable form that can be distributed quickly and widely through the postal system. There's no easy way to defend against that. If a terrorist did that, we'd just have to take the hit.

So it'd be better to find out that such a thing can be done by a serious terrorist organization or a hostile superpower? Or are you saying that only the US and its homegrown terrorists can figure out new ways to kill people?

I'm saying that only the U.S. military spent hundreds of millions of dollars, and gathered some of the most skilled scientists in the world, to figure out how to create biological weapons like weaponized anthrax.

The Japanese, Soviets, Iraqis, and a few local terrorist groups in the U.S. and Japan tried to create biological weapons, and they weren't successful. It's unlikely that anybody else would have applied the resources to the problem that the U.S. military did.

I'm saying that only the U.S. military spent hundreds of millions of dollars, and gathered some of the most skilled scientists in the world, to figure out how to create biological weapons like weaponized anthrax.

They weren't the only ones and as another replier noted [slashdot.org], the USSR probably put far more effort and resources into it.

The Japanese, Soviets, Iraqis, and a few local terrorist groups in the U.S. and Japan tried to create biological weapons, and they weren't successful. It's unlikely that anybody else would have applied the resources to the problem that the U.S. military did.

Not what I heard. The Soviets at least were thought to have a variety of humdingers. And the Iraqis were supposed to have a viable anthrax weapon in 1991.

Now that they've shown the way, it should be easy for a half-dozen microbiologists with a modest budget to reproduce their weaponized, easily dispersed anthrax.

As I attempted to say in my previously screwed up reply, would it be better to figure out what is possible so that you can guard against it or just get nastily surprised by some hostile power or terrorist group in the future? What you are cl

Because he knows what he's talking about and not one person has stepped forward to contradict his statement. And from what I've read, long before he's stepped forward, there had always been some question as to whether or not that lab could have even produced the quantity of Anthrax released. Based on his statements, it appears the FBI knew full well the lab couldn't have ever created that much Anthrax without the entire lab being in on it.

One thing that everybody agrees on is that the anthrax used in the attacks came from the USMRIID.

There's a very good substitution for no mod points; Refuting the spurious point with facts and logic, hopefully not only educating the OP who is misinformed, but increasing the knowledge of those who read your reply to the over-rated comment.

In fact, I wish people would refute the points using facts and logic than modding the incorrect information down. Then again, I wish everybody would vote, politicians weren't corrupt and power-hungry, and that life saving medications were given free of charge to those

Still, I'll note that while I have some training in responding to biological, as well as chemical and radiological attacks, my first thought was the potential medical benefits of this test.

Antibiotics are getting tougher, we even have a number of anti-virals. They're all targeted, and you don't want to give somebody them if you don't have to. When it comes to bacteria, there's whole listings of phages - but they each target like 1 bacterial strain.

Let's just call it the Microbial Detection Array. I mean, thanks a lot Lawrence Livermore, really, but do you really want a bunch of people going around saying "lambda" because that's how they're pronouncing that crazy acronym?

Let's just call it the Microbial Detection Array. I mean, thanks a lot Lawrence Livermore, really, but do you really want a bunch of people going around saying "lambda" because that's how they're pronouncing that crazy acronym?

It's about funding. The next time the funding for Lawrence Livermore comes up in Congress, it helps to have someone who can say: "Ah, yes, I have heard of them. Um, they make that detector . . . which I don't really understand what it does."

Sure, the number sounds impressive but it's still clinically worthless in 99.9% of situations. There are a relatively small number of infectious agents that are life-threatening, of those the likely culprit in most cases can be narrowed down to far fewer than 10 simply based on symptoms. Reimbursement is another issue with these multiplexed test since unless a doctor can demonstrate that looking for every single disease in the the test's repertoire was medically necessary, insurance companies won't fully re

From what I can see in the linked articles, it seems to be superior to classical multiplexing PCR in that it has a higher parallel detection capability. I agree, though, that this is not necessary in the vast majority of clinical situations. There still might be fringe cases where something like it could be used in a medical setting. However, I rather view it as a new, valuable research tool. Being able to quickly "population-type" a microbial environment could be very useful in a variety of fields. They ju

I agree, though, that this is not necessary in the vast majority of clinical situations. There still might be fringe cases where something like it could be used in a medical setting.

Right, this will be for one of those desperate cases that you read about in medical journals where they think they have an infection but they just can't identify it and empirical antibiotics aren't working. Its effectiveness will be limited by the false positives. How many commensal bacteria are there in the human body? 6,000? So the test says you've got 30 sometimes-pathogenic microbes. Then what do you do?

I rather view it as a new, valuable research tool. Being able to quickly "population-type" a microbial environment could be very useful in a variety of fields.

That could be one of the really useful applications. I'm sure the Human Microbiome Project will be ex

Not having read TFA, I could be wrong, but it sounds like an array-based detection system..

You absolutely cannot multiplex PCRs for that many targets, so it has to be an array, right?

There may be some non-specific PCR, or other form of 'amplification' i.e. in vitro transcription, done beforehand to amplify the starting matierial (in fact, this would probably be required since array sensitivity is crap compared to PCR).

TECHNICIAN: Next.Joe steps up. The Technician holds up three probes connected to the diagnostic machine.TECHNICIAN: Okay. This one goes in your mouth.Joe tentatively opens his mouth. The technician puts it in.TECHNICIAN: This one's for your ear.The technician sticks a second probe in Joe's ear.TECHNICIAN: And... This one goes in your butt.The technician hands Joe a third probe. Joe looks at it reluctantly, hesitates a beat, then looks at the line of 20 people staring at him.GUY IN LINE: Hurry UP ASSHOLE!!!Joe unhappily puts the plug up his butt.TECHNICIAN: Shit, wait a second.The Technician pulls all three plugs out and stupidly fumbles with the identical cables.TECHNICIAN: Okay, one goes in your... No, wait a second...Joe tries to follow the one that was in his butt like three card monte, but it's a lost cause. The technician stopsshuffling the probes.TECHNICIAN: Okay. This one goes in your mouth.Joe stares in horror as the Technician brings the probe closer to his mouth. Joe hesitates.GUY IN LINE: COME ON!!!

It takes out a mundane part of a doctors day to day practice. Doctors are still needed to administer treatment once the diagnosis is found, and to make sure that the treatment is working and not causing any adverse side effects.

I really despise this line of thinking. I deal with it on a daily basis where people will say, "If we use this awesome new technology that can HELP people, we're ALL GOING TO BE OUT OF JOBS@!!!!11111!"

What many people don't realize is that, for each job a technology MIGHT take away, others are created. For example, computers has made the need for personal secretaries to be much less necessary. However, computers have also created millions of more jobs (programmers, hardware designers/builders, computer r

In the old days a doctor would examine you, find the cause usually, and prescribe effective treatment based on user experience, patient preference, patient history, possible severity of infections, etc. Also a face to face encounter enables the prescribed treatment(s) to seem more important to the patient.

Sorry but I do not see the doctor phasing out anytime in the near future, if anything, from doctors I know, they would love a conclusive result so more patients could be seen and helped: our (unhealthy)-h

When they invent a machine that can outsmart a human in every way (not just be good at one thing, such as chess for instance) and closely replicate human insight and creativity, then doctors (more specifically, diagnosticians) will have something to worry about. By that

In the olden days doctors didn't know what you have so they just gave you antibiotics. That isn't too different from today, and it probably won't be much different in the future (identify and eliminate are separate problems), unless we figure out a way of eliminating common viruses, and even then we will probably have a new enemy, such as prions. Also, IMO, the majority of health concerns today in the western world are from lifestyle choices. It is hard to come up with a pill for fat and lazy, although we t

In the olden days (now) a doctor would examine at you and see what virus you probably had then order tests. But tomorrow if they can just scan for everything there's no need for doctors.:(

why the sad face? Where I live, doctors are simply an interface to their computer. If you cant fix it with pills then it doesn't exist. Doesn't matter what you go there for, they'll check your throat and ears.

As soon as you find a good doctor, chances are everyone else does too and then it becomes impossible to book an appointment because their schedule is always full, and then they invariably leave and go elsewhere...and the medical centre will never disclose where.

Doctors are just walking medical encyclopaedias anyway. I don't even recognise them as professionals; In the UK they're given the courtesy title of "Doctor" yet they don't necessarily have a doctorate.

I've started a little experiment; Every time I go to the doctor, I look up my symptoms on the web first. I don't tell the doctor I've done this, I don't offer suggestions, I do it out of curiosity. So far, I've a 100% correct diagnosis rate (my diagnosis is identical to his). I even get the name of the medica

Yes but the embarrassment of whipping out my "three-inch-long bio-detector" and then waiting "just 24 hours" for the results before continuing is going to ruin the mood. Oh you meant that kind of eating out. In that case I apologize for the worlds geekiest "your momma" joke. On on "Mothers Day" no less.

1) Some folks loudly and publicly claim birth control devices can't be used to prevent pregnancy because in the heat of the moment they are too inconvenient. Personally I think those people are making mating calls not accurately describing others. Regardless of who's personal life they're talking about, they'll use the same anti-marketing on this device.

We already have home tests here in the Netherlands. I work in the building above the STD testing facilities in Amsterdam, and every day there is a line of people wanting to get checked... not only because they think they've got something, but people are starting to get checked regularly, it isn't taboo here anymore. But especially to increase the test rate of younger people you can get a test kit at home now. I also received the letter for the Chlamydia check recently, when you answer they send you a test k

I live in the Netherlands and I didn't know about the home test:DAny idea where I can order one?Not for the anonymity (or I would check that box above this one) but for the ease of not having to take a free day/morning off from work for it.

Information about the free Chlamydia test can be found here: https://www.chlamydiatest.nl/ [chlamydiatest.nl]. The problem is it's the first time they do this and only works by invite now... If you live in Amsterdam, Rotterdam or Limburg and are between 16-29 you will be invited to participate. I do not know when other regions and ages will be able to participate...
Self tests are also available at some pharmacies, but please note the following warning: http://www.gezond.amsterdam.nl/Infectieziekten--hygine/SOA--HIV/Zelfteste [amsterdam.nl]

I hope they consider the effects of beneficial bacterial flora in the body and create an array that can test for them too. It would be interesting to compare symbiotic cultures that reduce the effect of pathogens. (Now that antibiotics are so much less effective. Let the bacteria duke it out among themselves.)

How is that useful in a biological or chemical attack? 11:05pm attack occurs, 11:06pm you've received lethal exposure to the biological attack, 11:05pm the next day...yep you're going to die to weaponized small pox alright. Or they could just use a chemical agent. After 24 hours they detect neither virus nor bacteria. Even if they could detect a chemical attack generally kills in a lot less than 24 hours.
How is this device even remarkable at all? If I bought 388,000 cable subscriptions I could totally D

I think the most useful application of systems like this (not necessarily this one) would be in research to identify the causes of disease. There has been a long-standing suspicion that bacterial or viral infections at least contribute to many diseases, from asthma to depression, but this has been difficult and costly to investigate on a large scale. The most infamous case is chronic fatigue syndrome, long suspected to be the result of a viral infection.
Don't forget that it wasn't until 1982 that we figur

What about just identifying any DNA in the patient's blood that's not the patient's? There would have to be tolerance for the DNA of all the other organisms that live in human bodies without harm (intestine bacteria, etc), but that would seem to be a smaller task than 2000 species.

Such a device could answer thoroughly the question of whether there's any infection at all. If the answer is "yes", then further tests can be done to identify the infection's specific cause. If it's no, diagnosis can quickly move

Because DNA probes don't work that way. Reassembling complete organism genomes is a non-trivial task; all the current methods rely on chopping DNA up into fragments, sequencing those fragments, and then reassembling the fragment sequences. Unless you have a complete sequence for that particular patient, which unfortunately isn't yet quite practical, you can't say for sure that a given fragment is "not patient."

What they're doing instead, it sounds like to me, is looking for known subsequences that are cha

Going to reply myself, to add something important I forgot to mention in the previous post: if you're looking for RNA viruses such as HIV, then to identify "not patient" you'd also need to have a sequence of the patient's entire genome, but also the entire transcriptome, i.e. all the RNA which can be transcribed from the patient's DNA (and then, often, post-processed in various ways which can alter the sequence.) This is a problem which is dramatically larger than "just" getting a complete DNA sequence.

The point of test like this is that it is a quick screen. If you think of DNA and RNA together as being the source code for an organism, these probes are basically regular expressions looking for stretches of DNA that match DNA/RNA sequences of pathogens - quick and easy.
In order to find "not the patient", we would need to know "the patient" DNA, which, aside from issues of definition, would have to start with PCR and sequencing of the person - not at all quick, and would have to be on file before the i

It wouldn't be too difficult (relative to this) to make something that reacted to any DNA that's not eukaryotic. But chances are, that there are a bunch of different little bacteria going through your blood. These bacteria just haven't been caught by your immune system yet, but aren't really doing any harm. There's no guarantee that these pathogens even harm humans, just that they've somehow ended up in your blood.

The device is not 3-inches long. The consumable portion is 3-inches long. This is like saying that my HP color printer is only 3 inches long: The printer is actually 2 feet long, but the cartridge is only 3 inches. Also, the odds are that it requires additional processing before it even gets to the device.

I'm not knocking what they have done -- just knocking the oversimplified press releases.